Fig. 6: Comparison of DNMT1 flanking preferences with genomic DNA methylation.
a Correlation of the DNMT1 flanking sequence preference (DNMT1) with genome-wide CpG methylation patterns in human cells (Genome) determined by whole genome bisulfite analysis in human ES cells39. The top image shows the average methylation levels of CpG sites with different NNCGNN flanks as heatmap. The p value of the correlation is 6.77 × 10−13. The lower image shows a box plot of the genomic methylation levels of CpG sites in defined ranges of DNMT1 preferences. The lines show the medians, the boxes show the 1st and 3rd quartile and the whiskers display the data maximum and minimum. b Correlation of the DNMT1 flanking sequence preference (DNMT1) with genome-wide CpG methylation patterns (Genome) determined by reduced representation genome bisulfite analysis in lung cancer cells41. The image shows the average methylation levels of CpG sites with different NNCGNN flanks as heatmaps and the corresponding box plot as described in (a). The p value of the correlation is 1.98 × 10−10. c Anticorrelation of the DNMT1 flanking sequence preference with genome-wide CpG demethylation after treatment of lung cancer cell with 5-azacytidine41. The image shows the DNMT1 preferences of NNCGNN flanks (DNMT1) and average levels of genome demethylation of CpG sites in NNCGNN flanks (Genome) as heatmaps and the corresponding box plot. Relative DNA demethylation is calculated as Δmethylation/initial methylation. The p value of the anticorrelation is 7.63 × 10−5. The p values of (anti)correlations in (a–c) were based on the Pearson correlation coefficients (r-factor) and the Z-statistics of the distribution of r-factors determined after randomization of one of the data sets. Source data are provided as a Source Data file.
